Align 2 faces with only two vertices and constraints
I'm confused with the question so here are a few options.
To flatten the faces on the $Z$ axis, for example, select all vertices, scale them to zero (press  S + Z+0)
You can modify the coordinates for any point numerically. Enter edit mode (↹ Tab) enable the Sidebar (press N) to access the Item Properties panel.
You can see the Local and Global coordinates and manipulate them at will.

So you can flatten the faces first and then, with all vertices still selected, you can set them at the correct coordinates numerically.

To move a vertex along an existing edge, use Vertex Slide (⇧ Shift+ V)